Everytime ActiveSync fires up, and if you have set Onenote to automatically
sync (copy) your notes from the device, OneNote compares what is on the
device with what you copied over last time. If anything is missing or
changed in your OneNote notebook "Copied from PocketPC" section, a new copy
of the original is copied into your notebook. User-modified notes remain in
OneNote and are unaffected by the new copy action, since these are no longer
representing what you brought from your machine (i.e. they are new and
different)
Chris Pratley (MS)
OneNote design team